One way to improve an algorithm for projecting a college quarterback's success in the pros would be to find out what good NFL quarterbacks excelled at in college. You could make a list of the ten best quarterbacks each year for the past decade, then dig up their college stats and see which area they excelled in. These areas would then be weighted more heavily in choosing which quarterback to draft.
However, I agree that player statistics can only tell you so much in this situation. The thing that matters most is in-person talent scouting, but I think a smart algorithm could be useful in providing another perspective. I'd like to see a study that illustrates how thorough in-person talent scouting relates to NFL franchise success.
And on the topic of recent football trends impacting all this, I'd say the variables are decreasing all the time because the college game is becoming more and more like the pros. College athletes are recruited like pros because now playing in a top program means heavily influencing where they get drafted, which means how much they get paid. College football is a big business and coaches are paid millions to win, so we are seeing more and more pro-style offenses, like the spread and the no-huddle. The game is also played faster and more physically, and teams are under a great amount of personal and career pressure, similar to the pros. All these factors plus the emergence of the wildcat offense in the NFL leads me to believe that teams will have an easier time evaluating which players will be successful in the pros. Look at the first three quarterbacks drafted two years ago: Matt Ryan and Joe Flacco are starters on teams that made the playoffs last year and currently have winning records, and Josh Freeman beat out two other quarterbacks to win a starting job on the awful Tampa Bay Buccaneers.

A few more thoughts on quarterbacks: There are two separate issues with respect to quarterbacks. The first is whether, historically, NFL teams have done a good job of predicting which college quarterbacks will succeed in the pros. Dave Berri and Rob Simmons’ paper in the Journal of Productiv...